[Chimera-users] how to solve the problem of topology

[Kenji MATSUI]

Dear Chimera

Thank you very much for your kind answers.

Sorry, I have a question about the issue of ligand topology for the docking
study.

The topology did not match when I used this ligand for the docking study.

Could you tell me how to solve this problem?

The thing I tried

1. I tried to add hydrogen atoms on UCSF Chimera by following the URL
below, but it did not work

Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html

2. Compare with the contents of the Mol2 file for cholesterol that was
correctly docked.

25-hydroxycho_only_0216
→ original file

25-hydroxycho_only_0216_Chimera
→after adding H using UCSF Chimera
---------------------------------------------------------------------------
松井 健治
 東京農工大学大学院 工学府産業技術専攻 修士
〒184-8588 東京都小金井市中町2-24-16
 Mail: s214903z at st.go.tuat.ac.jp

Kenji Matsui
 Graduate School of Tokyo University of Agriculture and Technology
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
 Mail: s214903z at st.go.tuat.ac.jp
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